Ceres, Inc.: Taming, Mapping, and Enhancing Genomes for Bioenergy

Jim Lane

Newly-public Ceres (CERE)
makes major breakthrough on miscanthus; is the gigantic energy
grass ready for prime-time? Why is miscanthus driving so much
attention, yet deserving more?

In California, followers of NASDAQ prices noted yesterday that
shares in the newly-public Ceres (CERE)
rocketed up 15 percent to close at $17.52. What happened? It was
revealed yesterday, in the peer-reviewed, online journal PLoS One
that Ceres and the Institute of Biological, Environmental and Rural
Sciences (IBERS) at Aberystwyth University in Wales have completed
the first high-resolution, comprehensive genetic map of miscanthus.
The full
article is here.

In other crops, this type of comprehensive genetic mapping has
significantly shortened product development timelines. Hence,
the lift in the stock.

Proving that money is not, as it turns out, the root of all evil.
Apparently, it can drive the attention of NASDAQ investors away from
the dramatics of The Kardashians or NCAA basketball and towards the
frontiers of science, in ways that ruler-slapping, ninth-grade
biology teachers can only dream of.

The breakthrough in miscanthus

As published in the journal article, Ceres researchers mapped all 19
chromosomes of miscanthus, a towering cane-like grass that can be
used as a feedstock for advanced biofuels, bio-based products and
power generation. The multi-year project involved generation and
analysis of more than 400 million DNA sequences creating a blueprint
of the genetic alphabet of the plant.

Among the massive volumes of data, researchers found 20,000 genetic
differences, called markers, that allow geneticists to differentiate
individual plants based on small variations in their DNA.

More than 3,500 of these markers were used to create the genetic
map, and are valuable for crop improvement purposes. In contrast,
previously announced mapping projects discovered only about 600
markers and did not fully characterize the structure of all the
miscanthus chromosomes, a necessary step in establishing a high-tech
plant breeding program. Previously, most miscanthus research had
been focused on field trials, and little was known about its
genetics.

A little more about miscanthus
giganteus

Miscanthus giganteus.
Photo: Pat Schmitz, via Wikipedia Commons

Ceres is not the only company pursuing miscanthus. Mendel has
developed high-performing elite varieties of Miscanthus that are
competitive in yield with the public varieties but which can be
propagated and scaled much more efficiently. That is,
propagated from seed instead of cuttings.

Mendel has just embarked on a 4-year trial of miscanthus, in
partnership with BP, with a goal of making that a key feedstock for
BP’s cellulosic ethanol expansion in the US and elsewhere.

Targets for improvement? Yield, stress tolerance (including water,
salt or nutrient or pathogen), control of plant shape and form,
flowering time, bulk-up rate for rapid planting and
propagation. More on Mendel’s
pioneering work, here.

Of wolves and fishmatoes

The progress is miscanthus reminds us that, in bioenergy, we are
rapidly progressing beyond the hunter-gatherer era, in which
investors, scientists, touts and policymakers hurtled between one
wild wolf of a next-gen feedstock and another – once there was wild
jatropha, then wild algae, then wild switchgrass, then wild king
grass – “aha, this is the wonder feedstock!…no this one is!…no, this
one is.”

Many of them were promoted as domesticated puppies when they were,
it turns out, wild wolves that we did not understand at all well as
agriculturalists.

Most of them have come under domestication programs, which starts
with hybridization, using Mendelan cross-breeding principles. It
works, but it can be slow – it has taken eighty years to boost US
corn yields from 30 to 160 bushels per acre through hybridization,
and the introduction of transgenic traits such as pesticide or
herbicide resistance.

Beyond hybridization, there are three basic methods of improvement.
There is the exploration of the opportunities within the existing
genome – for every organism has genes that are currently not
expressed (to use an easily understood example, the genes that
produce eye color), and switching existing genes on and off to
discover the optimal combinations, that’s the basic level of genetic
improvement.

Then, there is the field of activity generally known as directed
evolution. Here, scientists mutate genes at random, those mutations
are screened for valuable properties, and genetic winners in each
round of evolution are then themselves put through further rounds of
variation. Now, Nature herself produces variation by this method, so
consider it a sped-up, industrialized version of a natural process.

The last and most controversial activity is actively moving genetic
material from one organism to another in ways that are unlike the
processes of Nature. For example, there was an effort to make
tomatoes more resistant to cold by inserting genes from a
cold-resistant fish – making a fishmato (which in every other way
basically looks and tastes like a tomato, but underneath the hood,
so to speak, its a fishmato. And, parenthetically, offering some
sort of ethical challenge to vegans.

The Bottom Line

No matter the genetic approach a scientific team is taking, time is
the enemy. Time stretches out the ROI until the rate falls below the
risk threshold that justifies investment. Or simply kills patience,
or exposes R&D to the possibility of being overwhelmed by
competing discoveries. The cardinal principle of the Western film is
that the cavalry must arrive in time to save the settlers.

The best-known general accelerator of genetic improvement? Genetic
mapping. Once you see the genome in all its diversity, and mark the
areas of interest – crop improvement can come at accelerated rates.
Hence the excitement over the news from Ceres and IBERS.

Miscanthus, as we know, is a crop whose fans seem to grow even
faster than the skyscraper-like grass itself. Extravagant test
yields in the 25 ton per acre range have been reported by, for
example, Repreve Renewables, using a varietal known as Freedom
originally developed at Mississippi State.

With yields in those ranges, 2500-3300 gallon per acre yields are
possible with terrestrial crops, yields that today can only be
accomplished with that aquatic micro-wolf, micro-algae.

Are those numbers real? For the test plots, no reason to doubt the
data. But grown at scale, exposed to pests and sub-optimal
conditions in large-scale monocultures? Hmmm.

But the opportunities in, say, miscanthus, improve mightily when a
genetic map is at hand.